The effect of operating conditions (temperature and the partial pressures of H2 and CO) on the reaction rate of Fischer-Tropsch synthesis (FTS) were investigated by carrying out experiments according to a Box-Behnken design (BBD), and were mathematically modeled by using response surface methodology (RSM). The catalyst used was a nano-structured cobalt/manganese oxide catalyst, which was prepared by thermal decomposition. The rate of synthesis was measured in a fixed-bed micro reactor with $H_2/CO$ molar feed ratio of 0.32-3.11 and reactor pressure in the range of 3-9.33 bar at space velocity of $3600h^{-1}$ and a temperature range of 463.15-503.15 K, under differential conditions (CO conversion below 2%). The results indicated that in the present experimental setup, the temperature and the partial pressure of CO were the most significant variables affecting reaction rate. Based on statistical analysis the quadratic model of reaction rate of FTS was highly significant as p-value 0.0002.